That's happened to me, too. The manual lists some diagnostic interpretation to the flashes, for the "system warning indicator" (the red triangle). Most of them are benign. I think that during charging, one result will come up if the throttle is slightly engaged or the cutout switch is in the wrong position (but I'm speculating - I haven't interpreted the flashes when I did get them). It's supposed to be a quick sequence like morse code, like "1" and then "3" as two clusters of flashes that repeat, which the manual says means "Charger Connected" (with throttle not relaxed or the cutout switch on) so maybe that's what you're getting.
The BMS light (in the little plastic window in front of the bike behind the forks on the left side) more directly tells you about the battery rather than the bike state. It's more like a progress meter (but also shows another state when balancing cells).
